It’s all about sequences

Genomic analysis is, naturally, focussed on manipulation and interrogation of biological sequences. You might be dealing with a single sequence, or a collection of sequences. You might want to sample regions of sequences that are annotated using meta-data from a public database. You might have collections of sequences that are related, but not aligned. You might have sequences that are aligned, but unrelated. The number of possible permutations is enormous. cogent3 provides capabilities to handle these permutations. In this document, I describe the main objects concerned with sequences, their basic properties and relationships to each other and the motivation behind them.